The Experts below are selected from a list of 9381 Experts worldwide ranked by ideXlab platform
Dario Neri - One of the best experts on this subject based on the ideXlab platform.
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Selective fragments for the CREBBP bromodomain identified from an Encoded Self‑Assembly Chemical Library
ChemMedChem, 2020Co-Authors: Marco Catalano, Jörg Scheuermann, Mustafa Moroglu, Petra Balbi, Federica Mazzieri, James Clayton, Katrina H Andrews, Martina Bigatti, Stuart J Conway, Dario NeriAbstract:DNA-encoded Chemical libraries (DECLs) are collections of Chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i.e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i.e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore Encoded Self-Assembly Chemical (ESAC) Library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from Library selections showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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selective fragments for the crebbp bromodomain identified from an encoded self assembly Chemical Library
ChemMedChem, 2020Co-Authors: Marco Catalano, Jörg Scheuermann, Mustafa Moroglu, Petra Balbi, Federica Mazzieri, James Clayton, Katrina H Andrews, Martina Bigatti, Stuart J Conway, Dario NeriAbstract:DNA-encoded Chemical libraries (DECLs) are collections of Chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i.e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i.e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore Encoded Self-Assembly Chemical (ESAC) Library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from Library selections showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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dna compatible diazo transfer reaction in aqueous media suitable for dna encoded Chemical Library synthesis
Organic Letters, 2019Co-Authors: Adrian Girondamartinez, Dario Neri, Florent Samain, Etienne J DonckeleAbstract:DNA-encoded Chemical libraries (DECLs) are increasingly employed in hit discovery toward proteins of pharmaceutical interest. Protected amino acids are the most commonly used building blocks for the construction of DECLs; therefore, the expansion of reaction scope with the subsequent free amine is highly desired. Here, we developed a robust DNA-compatible diazo-transfer reaction using imidazole-1-sulfonyl azide tetrafluoroborate salt converting a wide range of primary amines into their corresponding azides in good to excellent yields.
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a focused dna encoded Chemical Library for the discovery of inhibitors of nad dependent enzymes
Journal of the American Chemical Society, 2019Co-Authors: Lik Hang Yuen, Dario Neri, Srikanta Dana, Samuel I Bloom, A G Thorsell, Anthony J Donato, Dmitri Kireev, H Schuler, Raphael M. FranziniAbstract:DNA-encoded Chemical libraries are increasingly used in pharmaceutical research because they enable the rapid discovery of synthetic protein ligands. Here we explored whether target-class focused DNA-encoded Chemical libraries can be cost-effective tools to achieve robust screening productivity for a series of proteins. The study revealed that a DNA-encoded Library designed for NAD+-binding pockets (NADEL) effectively sampled the Chemical binder space of enzymes with ADP-ribosyltransferase activity. The extracted information directed the synthesis of inhibitors for several enzymes including PARP15 and SIRT6. The high dissimilarity of NADEL screening fingerprints for different proteins translated into inhibitors that showed selectivity for their target. The discovery of patterns of enriched structures for six out of eight tested proteins is remarkable for a Library of 58 302 DNA-tagged structures and illustrates the prospect of focused DNA-encoded libraries as economic alternatives to large Library platforms.
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quantitative pcr is a valuable tool to monitor the performance of dna encoded Chemical Library selections
ChemBioChem, 2017Co-Authors: Yizhou Li, Gunther Zimmermann, Jörg Scheuermann, Dario NeriAbstract:: Phage-display libraries and DNA-encoded Chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial Chemical Library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
Jörg Scheuermann - One of the best experts on this subject based on the ideXlab platform.
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Selective fragments for the CREBBP bromodomain identified from an Encoded Self‑Assembly Chemical Library
ChemMedChem, 2020Co-Authors: Marco Catalano, Jörg Scheuermann, Mustafa Moroglu, Petra Balbi, Federica Mazzieri, James Clayton, Katrina H Andrews, Martina Bigatti, Stuart J Conway, Dario NeriAbstract:DNA-encoded Chemical libraries (DECLs) are collections of Chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i.e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i.e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore Encoded Self-Assembly Chemical (ESAC) Library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from Library selections showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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selective fragments for the crebbp bromodomain identified from an encoded self assembly Chemical Library
ChemMedChem, 2020Co-Authors: Marco Catalano, Jörg Scheuermann, Mustafa Moroglu, Petra Balbi, Federica Mazzieri, James Clayton, Katrina H Andrews, Martina Bigatti, Stuart J Conway, Dario NeriAbstract:DNA-encoded Chemical libraries (DECLs) are collections of Chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i.e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i.e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore Encoded Self-Assembly Chemical (ESAC) Library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from Library selections showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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a specific and covalent jnk 1 ligand selected from an encoded self assembling Chemical Library
Chemistry: A European Journal, 2017Co-Authors: Gunther Zimmermann, Jörg Scheuermann, Davor Bajic, Ulrike Rieder, Sara Vanetti, A Chaikuad, S Knapp, Martin MattarellaAbstract:We describe the construction of a DNA-encoded Chemical Library comprising 148 135 members, generated through the self-assembly of two sub-libraries, containing 265 and 559 members, respectively. The Library was designed to contain building blocks potentially capable of forming covalent interactions with target proteins. Selections performed with JNK1, a kinase containing a conserved cysteine residue close to the ATP binding site, revealed the preferential enrichment of a 2-phenoxynicotinic acid moiety (building block A82) and a 4-(3,4-difluorophenyl)-4-oxobut-2-enoic acid moiety (building block B272). When the two compounds were joined by a short PEG linker, the resulting bidentate binder (A82-L-B272) was able to covalently modify JNK1 in the presence of a large molar excess of glutathione (0.5 mm), used to simulate intracellular reducing conditions. By contrast, derivatives of the individual building blocks were not able to covalently modify JNK1 in the same experimental conditions. The A82-L-B272 ligand was selective over related kinases (BTK and GAK), which also contain targetable cysteine residues in the vicinity of the active site.
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quantitative pcr is a valuable tool to monitor the performance of dna encoded Chemical Library selections
ChemBioChem, 2017Co-Authors: Yizhou Li, Gunther Zimmermann, Jörg Scheuermann, Dario NeriAbstract:: Phage-display libraries and DNA-encoded Chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial Chemical Library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
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Quantitative PCR is a Valuable Tool to Monitor the Performance of DNA‐Encoded Chemical Library Selections
ChemBioChem, 2017Co-Authors: Yizhou Li, Gunther Zimmermann, Jörg Scheuermann, Dario NeriAbstract:: Phage-display libraries and DNA-encoded Chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial Chemical Library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
David M. Reif - One of the best experts on this subject based on the ideXlab platform.
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phenotypic screening of the toxcast Chemical Library to classify toxic and therapeutic mechanisms
Nature Biotechnology, 2014Co-Authors: Nicole C. Kleinstreuer, Mark Polokoff, Ellen L Berg, David M. Reif, Richard S Judson, Matthew T Martin, Ann M Richard, Thomas B Knudsen, Jian Yang, Robert J KavlockAbstract:Results from screening hundreds of compounds on panels of primary human cells supports the use of such data for Chemical safety testing.
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Phenotypic screening of the ToxCast Chemical Library to classify toxic and therapeutic mechanisms
Nature Biotechnology, 2014Co-Authors: Nicole C. Kleinstreuer, Mark Polokoff, Ellen L Berg, David M. Reif, Richard S Judson, Matthew T Martin, Ann M Richard, Thomas B Knudsen, Jian Yang, David J. DixAbstract:Addressing the safety aspects of drugs and environmental Chemicals has historically been undertaken through animal testing. However, the quantity of Chemicals in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important Chemical libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for Chemicals that disrupt physiologically important pathways. Chemical-response signatures for 87 endpoints covering molecular functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental Chemicals and 135 reference pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polypharmacology and potential off-target effects for many Chemicals that have limited or no toxicity information. The endpoints measured can be closely linked to in vivo outcomes, such as the upregulation of tissue factor in endothelial cell systems by compounds linked to the risk of thrombosis in vivo. Our results demonstrate that assaying complex biological pathways in primary human cells can identify potential Chemical targets, toxicological liabilities and mechanisms useful for elucidating adverse outcome pathways.
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zebrafish developmental screening of the toxcast phase i Chemical Library
Reproductive Toxicology, 2012Co-Authors: Stephanie Padilla, Nicole C. Kleinstreuer, Thomas B Knudsen, D Corum, Beth Padnos, D L Hunter, Andrew L Beam, Keith A Houck, Nisha S Sipes, David M. ReifAbstract:Abstract Zebrafish (Danio rerio) is an emerging toxicity screening model for both human health and ecology. As part of the Computational Toxicology Research Program of the U.S. EPA, the toxicity of the 309 ToxCast™ Phase I Chemicals was assessed using a zebrafish screen for developmental toxicity. All exposures were by immersion from 6–8 h post fertilization (hpf) to 5 days post fertilization (dpf); nominal concentration range of 1 nM–80 μM. On 6 dpf larvae were assessed for death and overt structural defects. Results revealed that the majority (62%) of Chemicals were toxic to the developing zebrafish; both toxicity incidence and potency was correlated with Chemical class and hydrophobicity (logP); and inter-and intra-plate replicates showed good agreement. The zebrafish embryo screen, by providing an integrated model of the developing vertebrate, compliments the ToxCast assay portfolio and has the potential to provide information relative to overt and organismal toxicity.
Sergey A Kozmin - One of the best experts on this subject based on the ideXlab platform.
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emulating the logic of monoterpenoid alkaloid biogenesis to access a skeletally diverse Chemical Library
Journal of Organic Chemistry, 2013Co-Authors: John S Scotti, Sergey A KozminAbstract:We have developed a synthetic strategy that mimics the diversity-generating power of monoterpenoid indole alkaloid biosynthesis. Our general approach goes beyond diversification of a single natural product-like substructure and enables production of a highly diverse collection of small molecules. The reaction sequence begins with rapid and highly modular assembly of the tetracyclic indoloquinolizidine core, which can be chemoselectively processed into several additional skeletally diverse structural frameworks. The general utility of this approach was demonstrated by parallel synthesis of two representative Chemical libraries containing 847 compounds with favorable physicoChemical properties to enable its subsequent broad pharmacological evaluation.
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creation and manipulation of common functional groups en route to a skeletally diverse Chemical Library
Proceedings of the National Academy of Sciences of the United States of America, 2011Co-Authors: Olesya A Ulanovskaya, Joseph Dundas, Jie Liang, Sergey A KozminAbstract:We have developed an efficient strategy to a skeletally diverse Chemical Library, which entailed a sequence of enyne cycloisomerization, [4 + 2] cycloaddition, alkene dihydroxylation, and diol carbamylation. Using this approach, only 16 readily available building blocks were needed to produce a representative 191-member Library, which displayed broad distribution of molecular shapes and excellent physicoChemical properties. This Library further enabled identification of a small molecule, which effectively suppressed glycolytic production of ATP and lactate in CHO-K1 cell line, representing a potential lead for the development of a new class of glycolytic inhibitors.
Nicole C. Kleinstreuer - One of the best experts on this subject based on the ideXlab platform.
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phenotypic screening of the toxcast Chemical Library to classify toxic and therapeutic mechanisms
Nature Biotechnology, 2014Co-Authors: Nicole C. Kleinstreuer, Mark Polokoff, Ellen L Berg, David M. Reif, Richard S Judson, Matthew T Martin, Ann M Richard, Thomas B Knudsen, Jian Yang, Robert J KavlockAbstract:Results from screening hundreds of compounds on panels of primary human cells supports the use of such data for Chemical safety testing.
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Phenotypic screening of the ToxCast Chemical Library to classify toxic and therapeutic mechanisms
Nature Biotechnology, 2014Co-Authors: Nicole C. Kleinstreuer, Mark Polokoff, Ellen L Berg, David M. Reif, Richard S Judson, Matthew T Martin, Ann M Richard, Thomas B Knudsen, Jian Yang, David J. DixAbstract:Addressing the safety aspects of drugs and environmental Chemicals has historically been undertaken through animal testing. However, the quantity of Chemicals in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important Chemical libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for Chemicals that disrupt physiologically important pathways. Chemical-response signatures for 87 endpoints covering molecular functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental Chemicals and 135 reference pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polypharmacology and potential off-target effects for many Chemicals that have limited or no toxicity information. The endpoints measured can be closely linked to in vivo outcomes, such as the upregulation of tissue factor in endothelial cell systems by compounds linked to the risk of thrombosis in vivo. Our results demonstrate that assaying complex biological pathways in primary human cells can identify potential Chemical targets, toxicological liabilities and mechanisms useful for elucidating adverse outcome pathways.
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zebrafish developmental screening of the toxcast phase i Chemical Library
Reproductive Toxicology, 2012Co-Authors: Stephanie Padilla, Nicole C. Kleinstreuer, Thomas B Knudsen, D Corum, Beth Padnos, D L Hunter, Andrew L Beam, Keith A Houck, Nisha S Sipes, David M. ReifAbstract:Abstract Zebrafish (Danio rerio) is an emerging toxicity screening model for both human health and ecology. As part of the Computational Toxicology Research Program of the U.S. EPA, the toxicity of the 309 ToxCast™ Phase I Chemicals was assessed using a zebrafish screen for developmental toxicity. All exposures were by immersion from 6–8 h post fertilization (hpf) to 5 days post fertilization (dpf); nominal concentration range of 1 nM–80 μM. On 6 dpf larvae were assessed for death and overt structural defects. Results revealed that the majority (62%) of Chemicals were toxic to the developing zebrafish; both toxicity incidence and potency was correlated with Chemical class and hydrophobicity (logP); and inter-and intra-plate replicates showed good agreement. The zebrafish embryo screen, by providing an integrated model of the developing vertebrate, compliments the ToxCast assay portfolio and has the potential to provide information relative to overt and organismal toxicity.